This research will be done primarily in Turkey at Bogazici University in collaboration with Professor Haliloglu as an extension of NIH grant # R01 GM65347-01: "Targeting Drug Resistance in HIV-1 Protease". HIV-1 protease is the target of the most effective anti-viral drugs for the treatment of HIV-1 infection. The protease is a prime target as it processes the Gag and GagPol polyproteins at ten sites and allows for maturation of the immature virion facilitating the spread of the virus. Drug resistance is a subtle change in the balance of recognition events between the relative affinity of the enzyme to bind inhibitors and its ability to bind and cleave substrates. Since HIV-1 protease binds substrates and inhibitors at the same active site, a change that alters inhibitor binding also alters substrate binding and can cause the sequences of the substrates to co-evolve. To overcome the changes that occur with drug resistance and ultimately develop the next generation of inhibitors a comprehensive study of sequence substitutions and corresponding structural alterations must be performed. The goal of the parent proposal ("Targeting Drug Resistance in HIV-1 Protease" R01 GM65347-01) is to elucidate these changes using experimental techniques. In this application, we are extending an existing collaboration with the laboratory of Professor Turkan Haliloglu at Bogazici University in Istanbul, Turkey. We will use computational threading methodologies on the crystal structures of HIV-1 protease substrate complexes (determined in the parent proposal) to predict the most likely sites of changes in substrate sequences might occur in response to drug resistant mutations in the protease gene. This project will complement the parent grant by quickly scanning which sets of substrate sequences are likely to be variable, and therefore interesting, for a given drug resistant HIV-1 protease variant. [unreadable] [unreadable] [unreadable]